Import and local transmission analysis

The input for this analysis is the results from the maximum likelihood mapping of the geographical states on the full phylogenetic tree of the 9732 genomes.

Import versus local transmission for Norway, Australia, Europe and the USA

From the mapped geographical lineage distributions we can derive the number of importation and local transmission events for each location (based on the available sequences). NB. we do not account for unobserved infections (sequences), and hence the estimated number only reflects the fraction of sequenced genomes that is assigned to specific lineages. The relative growth between the lineages (growth of an transmission lineage implies local transmission), is an important quantity and tells us how dominant specific lineages have become over time. This too could be affected by nonrandom sampling such as targeted sampling of lineages with anitibiotic resistance.

Cumulative growth of transmission lineages

The following plots show the cumulative number of sequences obtained from each estimated transmission lineage over time

name_date_NOR = name_date[name_date$name%in%nor_tips,]
linfo_NOR = lineage_info(Result_NOR,name_date = name_date_NOR)
LineageHomology::lineage_growth_cumulative(linfo_NOR,datelims=c("2015-01-01","2019-06-15","1 year"))

name_date_AUS = name_date[name_date$name%in%aus_tips,]
linfo_AUS = lineage_info(Result_AUS,name_date = name_date_AUS)
LineageHomology::lineage_growth_cumulative(linfo_AUS,datelims=c("2016-07-01","2018-06-15","5 months"))

name_date_USA = name_date[name_date$name%in%usa_tips,]
linfo_USA = lineage_info(Result_USA,name_date = name_date_USA)
LineageHomology::lineage_growth_cumulative(linfo_USA,datelims=c("2008-07-01","2019-06-15","2 year"))

name_date_EUR = name_date[name_date$name%in%eur_tips,]
linfo_EUR = lineage_info(Result_EUR,name_date = name_date_EUR)
LineageHomology::lineage_growth_cumulative(linfo_EUR,datelims=c("2008-07-01","2019-06-15","2 year"))

Aggregated estimates of import, local transmission and export over the full phylogeny:

c1 = Summarize_import_export_local_transmission(implocexp_NOR); c1
##                                                         2.5%          50%
## Import                                            706.850000  736.0000000
## Local transmission                               1929.425000 1967.5000000
## Export                                            922.475000  980.5000000
## Import / ( Import + Local transmission - export)    0.412446    0.4271619
##                                                         97.5%
## Import                                            764.0000000
## Local transmission                               2004.0500000
## Export                                           1028.0000000
## Import / ( Import + Local transmission - export)    0.4390678
c2 = Summarize_import_export_local_transmission(implocexp_AUS); c2
##                                                          2.5%          50%
## Import                                            356.4750000  371.5000000
## Local transmission                               2152.0000000 2175.0000000
## Export                                            312.4750000  346.0000000
## Import / ( Import + Local transmission - export)    0.1623292    0.1688253
##                                                         97.5%
## Import                                            391.0000000
## Local transmission                               2199.0500000
## Export                                            381.6750000
## Import / ( Import + Local transmission - export)    0.1770533
c3 = Summarize_import_export_local_transmission(implocexp_USA); c3
##                                                          2.5%          50%
## Import                                            370.9500000  390.0000000
## Local transmission                               2574.3750000 2595.5000000
## Export                                            586.9000000  617.0000000
## Import / ( Import + Local transmission - export)    0.1572872    0.1646612
##                                                         97.5%
## Import                                            407.5750000
## Local transmission                               2620.1000000
## Export                                            645.0000000
## Import / ( Import + Local transmission - export)    0.1710577
c3 = Summarize_import_export_local_transmission(implocexp_EUR); c3
##                                                          2.5%          50%
## Import                                            449.4750000  476.0000000
## Local transmission                               4233.9500000 4266.5000000
## Export                                            620.0000000  643.5000000
## Import / ( Import + Local transmission - export)    0.1106148    0.1161259
##                                                         97.5%
## Import                                            499.5250000
## Local transmission                               4306.0000000
## Export                                            662.0000000
## Import / ( Import + Local transmission - export)    0.1205556

In Norway we estimate that around 27% of locally observed cases can be attributed due to importation events.
This is more than twice that estimated for the other locations (Australia, the USA, and Europe in general).

Stratifying the estimates on the periods 2010-2014, 2014-2018, and 2010-2018 (total), we obtain the following estimates

By dividing importation and exportation by (import + local transmission) and (export + local transmission), respectively, we obtain the following estimates:

The fraction of total events that are imports, exports and local transmissions in the period 2000-2018 are visualized below.

#pdf("/Users/magnusnygardosnes/Dropbox/10000_Lovers/Junk_used_for_exploratory/Temp/imp_exp_loc_NOR.pdf", width = 10, height = 8)
plot_relative_fraction(implocexp_NOR)

#dev.off()

#pdf("/Users/magnusnygardosnes/Dropbox/10000_Lovers/Junk_used_for_exploratory/Temp/imp_exp_loc_AUS.pdf", width = 10, height = 8)
plot_relative_fraction(implocexp_AUS)

#dev.off()

#pdf("/Users/magnusnygardosnes/Dropbox/10000_Lovers/Junk_used_for_exploratory/Temp/imp_exp_loc_USA.pdf", width = 10, height = 8)
plot_relative_fraction(implocexp_USA)

#dev.off()


#pdf("/Users/magnusnygardosnes/Dropbox/10000_Lovers/Junk_used_for_exploratory/Temp/imp_exp_loc_EUR.pdf", width = 10, height = 8)
plot_relative_fraction(implocexp_EUR)

#dev.off()

The absolute estimates on the same periods are shown below.